But not all of my pages above pr 4 show up using link:www.mydomain.com. And the don't show up at all for link:mydomain.com.

I don't use flash or javascript or dhtml. They are dynamically generate on the server through php. I use absolute link paths for my most important links (if that even does anything but slow it down slightly).

I wouldn't worry about that at all. I don't show any links using that format either.

>>>and found only a few links from within my own site

Make sure the pages that you think should be showing(pr4 or higher) are actually indexed themselves. If you are using links with query strings(?id=value&page=anothervalue), it is possible they are not indexed. Sometimes google won't crawl those pages.